Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008743.1 Hibiscus syriacus cultivar Beakdansim tig00111832_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 979257
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 5
Found at i:3069 original size:104 final size:105
Alignment explanation
Indices: 2855--3619 Score: 1151
Period size: 104 Copynumber: 7.4 Consensus size: 105
2845 AGGTCTTACC
* * *
2855 CAGAGTCAATTTCAACTTCACAACGAATGATATTGAACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
2920 ACGAAGGGA--GCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* * * *
2958 CAGAGCCAATTTCCACTTCACGACAAAGGATATTGGACTCCAGAC-ACACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
3022 ACGAAGGGACCGCTAGTTGTCAATAAACATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
3062 CAGAGCCAATTTC-ACTTCACAACGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
3126 ACGAAGGGACCGCTGGTTGTCAACAAACATCTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
3166 CAGAGCCAATTTCAACTTCACAACG-AGGATATTGGACTCCAGACAATGCAAG-TCAACTTC-CG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
3228 ACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
3268 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAAACTTCAC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTC-AACTTCAC
* *
3333 GACGAAGGGACCGCTGGTTGTCCATAAACA--TCTCAATTT
65 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
3372 CAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTACAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
3437 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
3477 CAGAGCCAATTTCAACTCCACAACGAAGGATATTGGACTCCAGACAA--C-AGTTCAACTTCACA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
** * *
3539 ACGAAGGGATGGCTGGTTGTCAACAAACAATTTC-CCAGTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTT
* * * *
3579 CTAGAACCAATTTCAACTCCACGACGGAGGATATTGGACTC
1 C-AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
3620 GGAACAATAC
Statistics
Matches: 609, Mismatches: 41, Indels: 24
0.90 0.06 0.04
Matches are distributed among these distances:
102 135 0.22
103 179 0.29
104 195 0.32
105 70 0.11
106 30 0.05
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:3463 original size:311 final size:309
Alignment explanation
Indices: 2855--3619 Score: 1175
Period size: 311 Copynumber: 2.5 Consensus size: 309
2845 AGGTCTTACC
* * *
2855 CAGAGTCAATTTCAACTTCACAACGAATGATATTGAACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAA-GCAAGTTCAACTTCACG
* * *
2920 ACGAAGGGAGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCCACTTCACGACAAA
65 ACGAAGGGAGCTGGTTGTCAACAAACATTTCCCAATTTCAGAGCCAATTTCAACTTCACGACGAA
2985 GGATATTGGACTCCAGACACACAAGTTCAACTTCACGACGAAGGGACCGCTAGTTGTCAATAAAC
130 GGATATTGGACTCCAGACACACAAGTTCAACTTCACGACGAAGGGACCGCTAGTTGTCAATAAAC
* *
3050 ATTTCCCAATTTCAGAGCCAATTTCACTTCACAACGAATGATATTGGACTCCAGACAACGCAAGT
195 A-TTCCCAATTTCAGAGCCAATTTCACTTCACAACGAAGGATATTGGACTACAGACAACGCAAGT
3115 TCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATCTCTCAATTT
259 TCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATCTCTCAATTT
3166 CAGAGCCAATTTCAACTTCACAACG-AGGATATTGGACTCCAGACAATGCAAG-TCAACTTC-CG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAA-GCAAGTTCAACTTCACG
* *
3228 ACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACG
65 ACGAAGGGA--GCTGGTTGTCAACAAACATTTCCCAATTTCAGAGCCAATTTCAACTTCACGACG
* * *
3293 AAGGATATTGGACTCCAGACAACGCAAGTTCAAACTTCACGACGAAGGGACCGCTGGTTGTCCAT
128 AAGGATATTGGACTCCAGAC-ACACAAGTTC-AACTTCACGACGAAGGGACCGCTAGTTGTCAAT
* *
3358 AAACA-TCTCAATTTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTACAGACAACGC
191 AAACATTCCCAATTTCAGAGCCAATTTC-ACTTCACAACGAAGGATATTGGACTACAGACAACGC
*
3422 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
255 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATCTCTCAATTT
* *
3477 CAGAGCCAATTTCAACTCCACAACGAAGGATATTGGACTCCAGACAA-C-AGTTCAACTTCACAA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAGCAAGTTCAACTTCACGA
* * *
3540 CGAAGGGATGGCTGGTTGTCAACAAACAATTTCCC-AGTTCTAGAACCAATTTCAACTCCACGAC
66 CGAAGGGA--GCTGGTTGTCAACAAAC-ATTTCCCAATTTC-AGAGCCAATTTCAACTTCACGAC
*
3604 GGAGGATATTGGACTC
127 GAAGGATATTGGACTC
3620 GGAACAATAC
Statistics
Matches: 417, Mismatches: 27, Indels: 19
0.90 0.06 0.04
Matches are distributed among these distances:
308 11 0.03
309 10 0.02
310 123 0.29
311 174 0.42
312 99 0.24
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (309 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAGCAAGTTCAACTTCACGA
CGAAGGGAGCTGGTTGTCAACAAACATTTCCCAATTTCAGAGCCAATTTCAACTTCACGACGAAG
GATATTGGACTCCAGACACACAAGTTCAACTTCACGACGAAGGGACCGCTAGTTGTCAATAAACA
TTCCCAATTTCAGAGCCAATTTCACTTCACAACGAAGGATATTGGACTACAGACAACGCAAGTTC
AACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATCTCTCAATTT
Found at i:12390 original size:3 final size:3
Alignment explanation
Indices: 12384--12509 Score: 166
Period size: 3 Copynumber: 41.7 Consensus size: 3
12374 TCATTTAAAT
* *
12384 TTA TTA TTA TTA TTA -AA TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
12431 TTA TTA TTA TTA TTA GTA TTA TTA TTA TTA TAA TTA TTA TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
*
12477 TTA TTTA TTA TTA ATA -TA TATA TTA TTA TTA TT
1 TTA -TTA TTA TTA TTA TTA T-TA TTA TTA TTA TT
12510 TAAATATTAC
Statistics
Matches: 109, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
2 3 0.03
3 97 0.89
4 9 0.08
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:14684 original size:20 final size:21
Alignment explanation
Indices: 14661--14712 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
14651 AGAAATTAAA
14661 AATTCATTTATTT-AATTTTT
1 AATTCATTTATTTAAATTTTT
* *
14681 AATTCTTTTCTTTCAAATTTTT
1 AATTCATTTATTT-AAATTTTT
14703 -ATT-ATTTATT
1 AATTCATTTATT
14713 ATTTTTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 16 0.62
21 3 0.12
22 7 0.27
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (21 bp):
AATTCATTTATTTAAATTTTT
Found at i:23960 original size:54 final size:54
Alignment explanation
Indices: 23893--24156 Score: 404
Period size: 54 Copynumber: 4.9 Consensus size: 54
23883 AGAAATCTTG
* *
23893 GCAGAAGCCACAGTAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
1 GCAGAAGCTACAGTAAAAGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
23947 GCAGAAGCTACAGTAAAAGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
1 GCAGAAGCTACAGTAAAAGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
24001 GCAGAAGCTACAGTAAAAGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
1 GCAGAAGCTACAGTAAAAGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
* * * * * * * *
24055 ACAGAAACCACAGGAAAGGATGAATGTGTGGTCAAATATTTTATGAACATCTGA
1 GCAGAAGCTACAGTAAAAGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
* *
24109 GCAGAAG-TCACAGGAAAAGATGAATGTATTGTCAAATGTTTTACGAAC
1 GCAGAAGCT-ACAGTAAAAGATGAATGTGTTGTCAAATGTTTTACGAAC
24157 CAGTGATTAT
Statistics
Matches: 191, Mismatches: 18, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
54 191 1.00
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.26
Consensus pattern (54 bp):
GCAGAAGCTACAGTAAAAGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
Found at i:25348 original size:76 final size:76
Alignment explanation
Indices: 25205--26142 Score: 1794
Period size: 76 Copynumber: 12.4 Consensus size: 76
25195 CTATTTCCCA
25205 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
25269 AGCCTTCGGGT
66 AGCCTTCGGGT
25280 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
25345 AGCCTTCGGGT
66 AGCCTTCGGGT
*
25356 CATCTGTAAATCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC-GGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
25420 AGCCTTCGGGT
66 AGCCTTCGGGT
25431 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
25495 AGCCTTCGGGT
66 AGCCTTCGGGT
*
25506 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
25571 AGCCTTCGGGT
66 AGCCTTCGGGT
25582 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
25646 AGCCTTCGGGT
66 AGCCTTCGGGT
25657 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
25722 AGCCTTCGGGT
66 AGCCTTCGGGT
25733 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
25798 AGCCTTCGGGT
66 AGCCTTCGGGT
25809 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
25874 ATCCTTCGGGT
66 AGCCTTCGGGT
25885 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
25950 AGCCTTCGGGT
66 AGCCTTCGGGT
*
25961 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
26026 ATCCTTCGGGT
66 AGCCTTCGGGT
26037 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
26102 ATCCTTCGGGT
66 AGCCTTCGGGT
26113 CATCTGTAAGTCCTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTT
26143 TAAAACATTT
Statistics
Matches: 850, Mismatches: 9, Indels: 7
0.98 0.01 0.01
Matches are distributed among these distances:
75 255 0.30
76 595 0.70
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:26280 original size:3 final size:3
Alignment explanation
Indices: 26274--26410 Score: 202
Period size: 3 Copynumber: 44.7 Consensus size: 3
26264 TCATTTAAAT
** *
26274 TTA TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TTA GTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
26322 TTA TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA TATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
*
26368 TTA TTA TTA TTTA TTA TTA TTA ATA TTA TATA TTA TTA TTA TT
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TT
26411 TAAATATTAC
Statistics
Matches: 121, Mismatches: 10, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
3 112 0.93
4 9 0.07
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:30484 original size:30 final size:30
Alignment explanation
Indices: 30383--30542 Score: 133
Period size: 30 Copynumber: 5.3 Consensus size: 30
30373 CATATTCGAT
* * * *
30383 TTAAAGGACCAAAATAG-TAAAATAGAAAC
1 TTAAAGGACTAAAATAGCAAAAACAAAAAC
* * *
30412 TTAAAGAACTAAAATAGTAAAAACAAAAAAA
1 TTAAAGGACTAAAATAGCAAAAAC-AAAAAC
* * *
30443 TTAAAGTACTAAAATAGCAAAAACATAAAT
1 TTAAAGGACTAAAATAGCAAAAACAAAAAC
** *
30473 TTAAAGGACTAAAATAAAAAAAATAAAAAC
1 TTAAAGGACTAAAATAGCAAAAACAAAAAC
* * ** * *
30503 TTAAAAGACTAAAATAACAAAAGTAAACAG
1 TTAAAGGACTAAAATAGCAAAAACAAAAAC
30533 TTAAAGGACT
1 TTAAAGGACT
30543 GAACAGTAAA
Statistics
Matches: 107, Mismatches: 22, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
29 15 0.14
30 66 0.62
31 26 0.24
ACGTcount: A:0.63, C:0.09, G:0.09, T:0.19
Consensus pattern (30 bp):
TTAAAGGACTAAAATAGCAAAAACAAAAAC
Found at i:31403 original size:18 final size:16
Alignment explanation
Indices: 31368--31398 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31358 TGGTTTTTAT
*
31368 TTTTTTTGTTTGAATG
1 TTTTTTCGTTTGAATG
31384 TTTTTTCGTTTGAAT
1 TTTTTTCGTTTGAAT
31399 ATGTTGGGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.03, G:0.16, T:0.68
Consensus pattern (16 bp):
TTTTTTCGTTTGAATG
Found at i:44659 original size:35 final size:35
Alignment explanation
Indices: 44620--44690 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
44610 TGTTCAAAAA
*
44620 TCCAAAACACTTCAATTATATTCTAAGCCCTAAAT
1 TCCAAAACACTTCAATTATATTCTAAACCCTAAAT
* *
44655 TCCAAAATACTTTAATTATATTCTAAACCCTAAAT
1 TCCAAAACACTTCAATTATATTCTAAACCCTAAAT
44690 T
1 T
44691 GAAGTATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.41, C:0.23, G:0.01, T:0.35
Consensus pattern (35 bp):
TCCAAAACACTTCAATTATATTCTAAACCCTAAAT
Found at i:44726 original size:35 final size:35
Alignment explanation
Indices: 44686--44763 Score: 95
Period size: 35 Copynumber: 2.2 Consensus size: 35
44676 TCTAAACCCT
*
44686 AAATTGAAGTATTTTAAAATTTAGTGTTTAAAAT-
1 AAATTGAAGTATTTTAAAATTTAGGGTTTAAAATG
** * *
44720 ATAATTGATTTATTTTGAAATTTGGGGTTTAAAATG
1 A-AATTGAAGTATTTTAAAATTTAGGGTTTAAAATG
44756 AAATTGAA
1 AAATTGAA
44764 TACTGTGTTG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
34 1 0.03
35 34 0.94
36 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (35 bp):
AAATTGAAGTATTTTAAAATTTAGGGTTTAAAATG
Found at i:46053 original size:24 final size:24
Alignment explanation
Indices: 46021--46068 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
46011 AACGTCACAA
*
46021 ACGTTAGCACTTTAGTTGCCCGAG
1 ACGTTAGCACTTTAGTTACCCGAG
46045 ACGTTAGCACTTTAGTTACCCGAG
1 ACGTTAGCACTTTAGTTACCCGAG
46069 CCGTCAACAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.29
Consensus pattern (24 bp):
ACGTTAGCACTTTAGTTACCCGAG
Found at i:46601 original size:2 final size:2
Alignment explanation
Indices: 46552--46581 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
46542 TGTTTTTTAA
46552 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46582 TATTTTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46808 original size:28 final size:28
Alignment explanation
Indices: 46776--46834 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
46766 GAGTGAAATA
46776 TAATTGCCATTATTCAAAGAAAAAGGAT
1 TAATTGCCATTATTCAAAGAAAAAGGAT
46804 TAATTGCCATTATTCAAAGAAAAAGGAT
1 TAATTGCCATTATTCAAAGAAAAAGGAT
46832 TAA
1 TAA
46835 ATCAATTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.47, C:0.10, G:0.14, T:0.29
Consensus pattern (28 bp):
TAATTGCCATTATTCAAAGAAAAAGGAT
Found at i:51789 original size:48 final size:49
Alignment explanation
Indices: 51730--51831 Score: 170
Period size: 48 Copynumber: 2.1 Consensus size: 49
51720 TTATCATTTC
* * *
51730 CATCCAATTAAATATGAAACAAGATGAGTCCCACAAAACCCATCCCTTA
1 CATCCAATTAAATACGAAACAAGATGAATCCCACAAAACACATCCCTTA
51779 CATCC-ATTAAATACGAAACAAGATGAATCCCACAAAACACATCCCTTA
1 CATCCAATTAAATACGAAACAAGATGAATCCCACAAAACACATCCCTTA
51827 CATCC
1 CATCC
51832 TTATATTACG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
48 45 0.90
49 5 0.10
ACGTcount: A:0.43, C:0.30, G:0.07, T:0.20
Consensus pattern (49 bp):
CATCCAATTAAATACGAAACAAGATGAATCCCACAAAACACATCCCTTA
Found at i:52791 original size:200 final size:199
Alignment explanation
Indices: 52374--52813 Score: 598
Period size: 200 Copynumber: 2.2 Consensus size: 199
52364 TTCATACTAC
* * * * * *
52374 AAAAAA-TGTAGCACTTAACACGTACTTACATCGGTTTAAGTGAATAAAATAAACAAGTGTAACA
1 AAAAAAGTGTAGCACTTAACACATACTTACACCGATGTAAGTGAATAAAACAAAAAAGTGTAACA
* * * * * *
52438 CTTAATACATACTTACACCAATGTTAGTGAATAAAAAAAATGTAGCACTTAATACATATTACACC
66 CTTAACACATACTTACACCAATATAAGTAAATAAAAAAAATGTAGCACTTAACACATACTACACC
* * *
52503 GGTGTAAGTAAATAAAATAAACAAGTGTATCACTTAACACATACTTACACCGGTGTAGGTGAATA
131 GGTGTAAGTAAATAAAATAAACAAGTGTATCACTTAACACATACTTACAACGGTGTAAGTAAATA
52568 AAAT
196 AAAT
* * * *
52572 AAACAAGTGTAGTACTTAACACATATTTACACCGATGTAAGTGAATAAAACAAAAAAGTGTATCA
1 AAAAAAGTGTAGCACTTAACACATACTTACACCGATGTAAGTGAATAAAACAAAAAAGTGTAACA
** *
52637 CTTAACACATAC-TACACCGGTATAAGTAAATAAAATAAAAAATGTAGCACTTAACACATACTAT
66 CTTAACACATACTTACACCAATATAAGTAAAT--AA-AAAAAATGTAGCACTTAACACATACTAC
* * *
52701 ACCGGTGTAAGTGAATAAAATAAA-AATTGTATCTCTTAACACATACTTACAACGGTGTAAGTAA
128 ACCGGTGTAAGTAAATAAAATAAACAAGTGTATCACTTAACACATACTTACAACGGTGTAAGTAA
52765 ATAAAAT
193 ATAAAAT
*
52772 AAAAAAGTGTAACACTTAACACATACTTACACCGATGTAAGT
1 AAAAAAGTGTAGCACTTAACACATACTTACACCGATGTAAGT
52814 ATGTATATCT
Statistics
Matches: 209, Mismatches: 29, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
198 19 0.09
199 60 0.29
200 82 0.39
201 48 0.23
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.26
Consensus pattern (199 bp):
AAAAAAGTGTAGCACTTAACACATACTTACACCGATGTAAGTGAATAAAACAAAAAAGTGTAACA
CTTAACACATACTTACACCAATATAAGTAAATAAAAAAAATGTAGCACTTAACACATACTACACC
GGTGTAAGTAAATAAAATAAACAAGTGTATCACTTAACACATACTTACAACGGTGTAAGTAAATA
AAAT
Found at i:52814 original size:51 final size:51
Alignment explanation
Indices: 52374--52813 Score: 540
Period size: 51 Copynumber: 8.8 Consensus size: 51
52364 TTCATACTAC
* * *
52374 AAAAAA-TGTAGCACTTAACACGTACTTACATCGGTTTAAGTGAATAAAAT
1 AAAAAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAAAT
* * * ** *
52424 AAACAAGTGTAACACTTAATACATACTTACACCAATGTTAGTGAAT--AA-
1 AAAAAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAAAT
* *
52472 AAAAAA-TGTAGCACTTAATACATA-TTACACCGGTGTAAGTAAATAAAAT
1 AAAAAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAAAT
* * *
52521 AAACAAGTGTATCACTTAACACATACTTACACCGGTGTAGGTGAATAAAAT
1 AAAAAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAAAT
* * * * *
52572 AAACAAGTGTAGTACTTAACACATATTTACACCGATGTAAGTGAATAAAAC
1 AAAAAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAAAT
* * *
52623 AAAAAAGTGTATCACTTAACACATAC-TACACCGGTATAAGTAAATAAAAT
1 AAAAAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAAAT
*
52673 AAAAAA-TGTAGCACTTAACACATAC-TATACCGGTGTAAGTGAATAAAAT
1 AAAAAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAAAT
* * * * *
52722 -AAAAATTGTATCTCTTAACACATACTTACAACGGTGTAAGTAAATAAAAT
1 AAAAAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAAAT
* *
52772 AAAAAAGTGTAACACTTAACACATACTTACACCGATGTAAGT
1 AAAAAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGT
52814 ATGTATATCT
Statistics
Matches: 333, Mismatches: 48, Indels: 17
0.84 0.12 0.04
Matches are distributed among these distances:
46 16 0.05
47 17 0.05
48 12 0.04
49 63 0.19
50 68 0.20
51 157 0.47
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.26
Consensus pattern (51 bp):
AAAAAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAAAT
Found at i:69698 original size:19 final size:19
Alignment explanation
Indices: 69653--69706 Score: 81
Period size: 20 Copynumber: 2.8 Consensus size: 19
69643 CTATTCCCTA
*
69653 GTAATCTTACATTCTCACT
1 GTAATCTTACATTCCCACT
*
69672 GATAATCTTTCATTCCCACT
1 G-TAATCTTACATTCCCACT
69692 GTAATCTTACATTCC
1 GTAATCTTACATTCC
69707 GTGAACCAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.26, C:0.28, G:0.06, T:0.41
Consensus pattern (19 bp):
GTAATCTTACATTCCCACT
Found at i:69888 original size:28 final size:28
Alignment explanation
Indices: 69835--69893 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
69825 CCCTCAATTC
* **
69835 TTTTATATTTATAATTACTGTCCTTAAT
1 TTTTATATTTATAATGACTAACCTTAAT
69863 TTTTATATTTATAATGA-TAACTCTTAAT
1 TTTTATATTTATAATGACTAAC-CTTAAT
69891 TTT
1 TTT
69894 ATAATTTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 2 0.07
28 25 0.93
ACGTcount: A:0.31, C:0.08, G:0.03, T:0.58
Consensus pattern (28 bp):
TTTTATATTTATAATGACTAACCTTAAT
Found at i:70454 original size:17 final size:18
Alignment explanation
Indices: 70415--70464 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
70405 TCTTTTATCG
* *
70415 TGTTATAATATTATTTGT
1 TGTTATTATATTATTTCT
70433 T-TTATTAT-TTATTTCT
1 TGTTATTATATTATTTCT
70449 TGTTATTACTATTATT
1 TGTTATTA-TATTATT
70465 AACATCCTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 8 0.30
17 12 0.44
18 2 0.07
19 5 0.19
ACGTcount: A:0.24, C:0.04, G:0.06, T:0.66
Consensus pattern (18 bp):
TGTTATTATATTATTTCT
Found at i:71035 original size:2 final size:2
Alignment explanation
Indices: 71030--71055 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
71020 CCACACATGA
71030 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
71056 GGATGGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:72635 original size:19 final size:19
Alignment explanation
Indices: 72600--72640 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
72590 TAATAAATTT
72600 TAAAAATATAAATTAATCAAA
1 TAAAAATAT-AATTAAT-AAA
72621 TAAAAATAT-ATTAATAAA
1 TAAAAATATAATTAATAAA
72639 TA
1 TA
72641 TTAAATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 5 0.25
19 6 0.30
21 9 0.45
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAAATATAATTAATAAA
Found at i:84219 original size:22 final size:21
Alignment explanation
Indices: 84177--84216 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
84167 GAGTTTATTT
*
84177 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
84198 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
84217 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:92399 original size:2 final size:2
Alignment explanation
Indices: 92392--92418 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
92382 ACCACTACAC
92392 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
92419 GATCTTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:92972 original size:13 final size:14
Alignment explanation
Indices: 92952--92992 Score: 59
Period size: 13 Copynumber: 3.1 Consensus size: 14
92942 CACCAAAACC
92952 ACGAGCAAGCAACG
1 ACGAGCAAGCAACG
92966 A-GAGCAAGCAACG
1 ACGAGCAAGCAACG
*
92979 ACGACCAA-CAACG
1 ACGAGCAAGCAACG
92992 A
1 A
92993 AAAGAAGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 19 0.76
14 6 0.24
ACGTcount: A:0.46, C:0.29, G:0.24, T:0.00
Consensus pattern (14 bp):
ACGAGCAAGCAACG
Found at i:94126 original size:126 final size:125
Alignment explanation
Indices: 94013--94236 Score: 335
Period size: 126 Copynumber: 1.8 Consensus size: 125
94003 AAAAATAATC
*
94013 ATATTTT-GATATTTATTTATTTTT-AATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGC
1 ATATTTTGGATATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGC
** *
94076 TCTTTTCTGATATTTTTAAATAAATAAATATCTTATTAAAATAAATTTTTATTTTAAGAAA
66 TCTTTTCTGATATTTTTAAATAAATAAATATCTTATTAAAATAAATTTTTA-TAGAAAAAA
* * * * *
94137 ATGTTTTGGTTATTTATTTATTTTTCAATATCAAAGAAAAGAGTTGTCTTAAGGTACCTATAAGC
1 ATATTTTGGATATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGC
*
94202 TCTTTTCTGATATTTTTGAATAAATAAATATCTTA
66 TCTTTTCTGATATTTTTAAATAAATAAATATCTTA
94237 CTATATTAAA
Statistics
Matches: 91, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
124 6 0.07
125 16 0.18
126 69 0.76
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (125 bp):
ATATTTTGGATATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGC
TCTTTTCTGATATTTTTAAATAAATAAATATCTTATTAAAATAAATTTTTATAGAAAAAA
Found at i:94266 original size:115 final size:115
Alignment explanation
Indices: 94134--94351 Score: 319
Period size: 115 Copynumber: 1.9 Consensus size: 115
94124 TTATTTTAAG
* * * * *
94134 AAAATGTTTTGGTTATTTATTTATTTTTCAATATCAAAGAAAAGAGTTGTCTTAAGGTACCTATA
1 AAAATGTTTTGGATATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGA
* * * *
94199 AGCTCTTTTCTGATATTTTTGAATAAATAAATATCTTACTATATTAAAAT
66 AGCCCTTTTCTAATATTTCTAAATAAATAAATATCTTACTATATTAAAAT
* * *
94249 AAAATGTTTTTGATATTTATTTATTTTTTAATATCAAAGAAAATAGCTGTCTTAAAGCACCTAGA
1 AAAATGTTTTGGATATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGA
*
94314 AGCCCTTTTCTAATATTTCTAAATAAGTAAATATCTTA
66 AGCCCTTTTCTAATATTTCTAAATAAATAAATATCTTA
94352 TTTATGTATA
Statistics
Matches: 90, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
115 90 1.00
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (115 bp):
AAAATGTTTTGGATATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGA
AGCCCTTTTCTAATATTTCTAAATAAATAAATATCTTACTATATTAAAAT
Found at i:96056 original size:17 final size:17
Alignment explanation
Indices: 96034--96068 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
96024 GGTCACCAAG
*
96034 CTGAAAAATAACTGCAA
1 CTGAAAAAGAACTGCAA
96051 CTGAAAAAGAACTGCAA
1 CTGAAAAAGAACTGCAA
96068 C
1 C
96069 ATATATGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.51, C:0.20, G:0.14, T:0.14
Consensus pattern (17 bp):
CTGAAAAAGAACTGCAA
Found at i:104052 original size:76 final size:76
Alignment explanation
Indices: 103926--104067 Score: 239
Period size: 76 Copynumber: 1.9 Consensus size: 76
103916 CTATTTCCCA
* *
103926 CATCTGTAAGTCCTACAGTGTATGATGATTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTATAAGTCCTACAGTGCATGATGATTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
103991 AGCCTTAGGGT
66 AGCCTTAGGGT
* * *
104002 CATCTATAAGTCCTATAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAA
1 CATCTATAAGTCCTACAGTGCATGATGATTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
104067 A
66 A
104068 ACTTTCGAGT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
76 61 1.00
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (76 bp):
CATCTATAAGTCCTACAGTGCATGATGATTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:104098 original size:76 final size:76
Alignment explanation
Indices: 103929--104107 Score: 236
Period size: 76 Copynumber: 2.4 Consensus size: 76
103919 TTTCCCACAT
* * *
103929 CTGTAAGTCCTACAGTGTATGATGATTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGC
1 CTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAAC
* *
103994 CTTAGGGTCAT
66 CTTAGAGTCAA
* * *
104005 CTATAAGTCCTATAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAAAAC
1 CTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAAC
* *
104070 TTTCGAGTCAA
66 CTTAGAGTCAA
104081 CTGTAAG-CCTTACAGTGCA-GAATGTTT
1 CTGTAAGTCC-TACAGTGCATG-ATGTTT
104108 TTTTATTATT
Statistics
Matches: 89, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
75 3 0.03
76 86 0.97
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (76 bp):
CTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAAC
CTTAGAGTCAA
Found at i:104430 original size:114 final size:113
Alignment explanation
Indices: 104132--104550 Score: 646
Period size: 113 Copynumber: 3.7 Consensus size: 113
104122 AAACATTTCC
* *
104132 AGGTAGAGTTCATAATGAGAATAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAAC
1 AGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAAAAGTTCATAATGAGAAGAAC
*
104197 TTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTACT
66 TTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTACA
* *
104245 AGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAATGAAGAAAAAGTTCATAATGAGAAGAAC
1 AGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAAAAGTTCATAATGAGAAGAAC
* *
104310 TTGTTCAAGTTTTCACTTGAATTCATCATTCGATGGATCAGCATTACGA
66 TTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTAC-A
*
104359 AGGTAAAGTTCATAATGAGAAGAACTCATCTGAAG-AAGAAAGAAAAAGTTCATAATGAGAAGAA
1 AGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAG-AAGAAAAAGTTCATAATGAGAAGAA
** *
104423 CTTGTTCAACCTTTT-GCTTGAATTCATCATTCGATGGATCAATATTGCCA
65 CTTGTTCAA-CTTTTCGCTTGAATTCATCATTCGATGGATCAGCATT-ACA
* *
104473 A-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAAC
1 AGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAAAAGTTCATAATGAGAAGAAC
*
104537 TTGTTAAACCTTTT
66 TTGTTCAA-CTTTT
104551 GCTCGACTCT
Statistics
Matches: 282, Mismatches: 19, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
113 177 0.63
114 100 0.35
115 5 0.02
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.28
Consensus pattern (113 bp):
AGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAAAAGTTCATAATGAGAAGAAC
TTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTACA
Found at i:104535 original size:227 final size:227
Alignment explanation
Indices: 104132--104541 Score: 680
Period size: 227 Copynumber: 1.8 Consensus size: 227
104122 AAACATTTCC
* * *
104132 AGGTAGAGTTCATAATGAGAATAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAAC
1 AGGTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAAAAGTTCATAATGAGAAGAAC
* * * *
104197 TTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTACTAGGTCGAGTTCATAATG
66 TTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAACATTACCAAGTAGAGTTCATAATG
* *
104262 AGAAGAACTCATCTGAAGAATGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAAGTTTTCACT
131 AGAAGAACTCATCTGAAGAAAGAAGAAAAAGTTCATAATAAGAAGAACTTGTTCAAGTTTTCACT
104327 TGAATTCATCATTCGATGGATCAGCATTACGA
196 TGAATTCATCATTCGATGGATCAGCATTACGA
104359 AGGTAAAGTTCATAATGAGAAGAACTCATCTGAAG-AAGAAAGAAAAAGTTCATAATGAGAAGAA
1 AGGTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAG-AAGAAAAAGTTCATAATGAGAAGAA
* *
104423 CTTGTTCAACCTTTT-GCTTGAATTCATCATTCGATGGATCAATATTGCCAAGTAGAGTTCATAA
65 CTTGTTCAA-CTTTTCGCTTGAATTCATCATTCGATGGATCAACATTACCAAGTAGAGTTCATAA
*
104487 TGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTT
129 TGAGAAGAACTCATCTGAAGAAAGAAGAAAAAGTTCATAATAAGAAGAACTTGTT
104542 AAACCTTTTG
Statistics
Matches: 169, Mismatches: 12, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
226 3 0.02
227 161 0.95
228 5 0.03
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.28
Consensus pattern (227 bp):
AGGTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAAAAGTTCATAATGAGAAGAAC
TTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAACATTACCAAGTAGAGTTCATAATG
AGAAGAACTCATCTGAAGAAAGAAGAAAAAGTTCATAATAAGAAGAACTTGTTCAAGTTTTCACT
TGAATTCATCATTCGATGGATCAGCATTACGA
Found at i:104680 original size:123 final size:124
Alignment explanation
Indices: 104478--104883 Score: 593
Period size: 123 Copynumber: 3.3 Consensus size: 124
104468 TGCCAAGTAG
* * * *
104478 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
* *
104543 AACCTTTTGCTCGACTCTATCCCAGAAGGAGATAAATCAGCATCAACATTTCCAGAGAA
66 AACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAGCATCAACATTTCCAGAGAA
* *
104602 AGTTCATAATGGGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATGATAAGAGCTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
** * *
104666 AACCTTTTGCTCGACTCTATCGTAGAAGGAGATAGATCAGCATCAA-TTTTTCAGAGAA
66 AACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAGCATCAACATTTCCAGAGAA
104724 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
* * * * * * * *
104789 AACC-TTTGTTTGATTCTATCACAGAATGAGATAGATCAGTATCAGCATTTCCATAAAA
66 AACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAGCATCAACATTTCCAGAGAA
* *
104847 AGTTCATAATAAGAAGAACTCATCTAAAGAAGGAAGA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
104884 GAATTTGTTC
Statistics
Matches: 253, Mismatches: 27, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
122 71 0.28
123 154 0.61
124 28 0.11
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (124 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
AACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAGCATCAACATTTCCAGAGAA
Found at i:105068 original size:17 final size:16
Alignment explanation
Indices: 105046--105105 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 16
105036 CAACTTTGCC
105046 AGAAGAAGTTCATAATG
1 AGAAGAAGTTC-TAATG
*
105063 AGAAGAACTCCTCTGAA-G
1 AGAAGAAGT--TCT-AATG
105081 AAGAAGAAGTTCGTAATG
1 -AGAAGAAGTTC-TAATG
105099 AGAAGAA
1 AGAAGAA
105106 CTTATTCAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
17 19 0.54
18 4 0.11
19 12 0.34
ACGTcount: A:0.47, C:0.10, G:0.25, T:0.18
Consensus pattern (16 bp):
AGAAGAAGTTCTAATG
Found at i:105649 original size:13 final size:14
Alignment explanation
Indices: 105629--105669 Score: 59
Period size: 13 Copynumber: 3.1 Consensus size: 14
105619 CACCAAAACC
105629 ACGAGCAAGCAACG
1 ACGAGCAAGCAACG
105643 A-GAGCAAGCAACG
1 ACGAGCAAGCAACG
*
105656 ACGACCAA-CAACG
1 ACGAGCAAGCAACG
105669 A
1 A
105670 AAAGAAGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 19 0.76
14 6 0.24
ACGTcount: A:0.46, C:0.29, G:0.24, T:0.00
Consensus pattern (14 bp):
ACGAGCAAGCAACG
Found at i:106813 original size:126 final size:125
Alignment explanation
Indices: 106700--106923 Score: 353
Period size: 126 Copynumber: 1.8 Consensus size: 125
106690 AAAAATAATC
* *
106700 ATATTTT-GATATTTATTTATTTTT-AATATCGAAGAAAAGAGTTGTCTTAAGGCACCTAGAAGC
1 ATATTTTGGATATTTATTTATTTTTCAATATCAAAGAAAAAAGTTGTCTTAAGGCACCTAGAAGC
** *
106763 TCTTTTCTGATATTTTTAAATAAATAAATATCTTATTAAAATAAATTTTTATTTTAAGAAA
66 TCTTTTCTGATATTTTTAAATAAATAAATATCTTATTAAAATAAATTTTTA-TAGAAAAAA
* *
106824 ATATTTTGGTTATTTATTTATTTTTCAATATCAAAGAAAAAAGTTGTCTTAAGGTACCTAGAAGC
1 ATATTTTGGATATTTATTTATTTTTCAATATCAAAGAAAAAAGTTGTCTTAAGGCACCTAGAAGC
*
106889 TCTTTTCTGATATTTTTGAATAAATAAATATCTTA
66 TCTTTTCTGATATTTTTAAATAAATAAATATCTTA
106924 CTATATTAAA
Statistics
Matches: 93, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
124 7 0.08
125 16 0.17
126 70 0.75
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.45
Consensus pattern (125 bp):
ATATTTTGGATATTTATTTATTTTTCAATATCAAAGAAAAAAGTTGTCTTAAGGCACCTAGAAGC
TCTTTTCTGATATTTTTAAATAAATAAATATCTTATTAAAATAAATTTTTATAGAAAAAA
Found at i:109914 original size:52 final size:52
Alignment explanation
Indices: 109850--109960 Score: 152
Period size: 52 Copynumber: 2.1 Consensus size: 52
109840 TAATCCTGTC
* * *
109850 TATATCAAAGTTTAAAATGATTGTCGAAATATATATTCTTAGAAATTTC-ATT
1 TATATCAAAGTTTAAAATGATTGTCAAAATATATATGCATAG-AATTTCAATT
* * *
109902 TATATCAGAGTTTAAAATGATTTTCAAAATATTTATGCATAGAATTTCAATT
1 TATATCAAAGTTTAAAATGATTGTCAAAATATATATGCATAGAATTTCAATT
109954 TATATCA
1 TATATCA
109961 TAGTAGAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
51 6 0.12
52 46 0.88
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.42
Consensus pattern (52 bp):
TATATCAAAGTTTAAAATGATTGTCAAAATATATATGCATAGAATTTCAATT
Found at i:111716 original size:45 final size:44
Alignment explanation
Indices: 111653--111743 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 44
111643 AGAATATGTT
111653 TTCTTACCCATGGATTTAAGCTCCGTATGGGCCGCCATGGAAGA
1 TTCTTACCCATGGATTTAAGCTCCGTATGGGCCGCCATGGAAGA
111697 TTCTTACCCCATGGATTTAAGCTCCGTATGGGCCGCCATGGAAGA
1 TTCTTA-CCCATGGATTTAAGCTCCGTATGGGCCGCCATGGAAGA
111742 TT
1 TT
111744 GCCAGAGGCT
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 6 0.13
45 40 0.87
ACGTcount: A:0.22, C:0.25, G:0.24, T:0.29
Consensus pattern (44 bp):
TTCTTACCCATGGATTTAAGCTCCGTATGGGCCGCCATGGAAGA
Found at i:114126 original size:34 final size:35
Alignment explanation
Indices: 114073--114152 Score: 108
Period size: 34 Copynumber: 2.3 Consensus size: 35
114063 TTAATACGAT
*
114073 TAATAACAGTCATTTGAAGAACTAACTACCTACTC
1 TAATAACAGTCATTGGAAGAACTAACTACCTACTC
* * *
114108 TAAT-ACAGTGATTGGAAGAACTAAGTACCTACTT
1 TAATAACAGTCATTGGAAGAACTAACTACCTACTC
*
114142 TAATGACAGTC
1 TAATAACAGTC
114153 GTTCCACCAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
34 30 0.77
35 9 0.23
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.29
Consensus pattern (35 bp):
TAATAACAGTCATTGGAAGAACTAACTACCTACTC
Found at i:114654 original size:18 final size:19
Alignment explanation
Indices: 114620--114658 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
114610 GTAAATATAA
*
114620 AACATTTTATTATAAAATT
1 AACATTTAATTATAAAATT
114639 AACATTTAATTA-AAAATT
1 AACATTTAATTATAAAATT
114657 AA
1 AA
114659 AATTAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
AACATTTAATTATAAAATT
Found at i:114808 original size:60 final size:60
Alignment explanation
Indices: 114723--114839 Score: 189
Period size: 60 Copynumber: 1.9 Consensus size: 60
114713 AATGATCCCT
*
114723 TGACTATAGGATATTGCTTTATTAAGTCCATCGACTATTAAAAGTTACAAAATGGTCCTC
1 TGACTATAGAATATTGCTTTATTAAGTCCATCGACTATTAAAAGTTACAAAATGGTCCTC
* * * *
114783 TGACTATAGAATGTTGTTTTGTTAAGTCCCTCGACTATTAAAAGTTACAAAATGGTC
1 TGACTATAGAATATTGCTTTATTAAGTCCATCGACTATTAAAAGTTACAAAATGGTC
114840 ACCCGACTAT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.36
Consensus pattern (60 bp):
TGACTATAGAATATTGCTTTATTAAGTCCATCGACTATTAAAAGTTACAAAATGGTCCTC
Found at i:115039 original size:31 final size:29
Alignment explanation
Indices: 115004--115062 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
114994 AATATCGTCA
115004 ATTTTGGAACATAGTGAATAGTCGAGTGACC
1 ATTTTGGAAC-T-GTGAATAGTCGAGTGACC
* * *
115035 ATTTTGTAACTTTTAATAGTCGAGTGAC
1 ATTTTGGAACTGTGAATAGTCGAGTGAC
115063 TCAACAAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 15 0.60
30 1 0.04
31 9 0.36
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.36
Consensus pattern (29 bp):
ATTTTGGAACTGTGAATAGTCGAGTGACC
Found at i:115839 original size:26 final size:26
Alignment explanation
Indices: 115761--115842 Score: 119
Period size: 26 Copynumber: 3.1 Consensus size: 26
115751 AATAATTTTC
* *
115761 AAATAAATTTCGATTTGATTAACGGTC
1 AAAT-AATTTCGATTCGATTAACGGTT
115788 AAATAATTTCGATTCGATTAACGGTT
1 AAATAATTTCGATTCGATTAACGGTT
* *
115814 AAATAATTTCGGTTCGATTAATGGTT
1 AAATAATTTCGATTCGATTAACGGTT
115840 AAA
1 AAA
115843 GAAAAAAAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
26 47 0.92
27 4 0.08
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.38
Consensus pattern (26 bp):
AAATAATTTCGATTCGATTAACGGTT
Found at i:115887 original size:121 final size:119
Alignment explanation
Indices: 115695--115914 Score: 309
Period size: 121 Copynumber: 1.8 Consensus size: 119
115685 AACAATTTTC
* * *
115695 AAATAAATTTCGGTTCGATTAACGGTTAAGGAAAAAATAATTTATTTTATTTGGTTAATAATTTT
1 AAATAAATTTCGGTTCGATTAACGGTTAAAGAAAAAATAATTTATTTGATTCGGTTAATAATTTT
*
115760 CAAATAAATTTCGATTTGATTAACGGTCAAATAATTTCGATTCGATTAACGGTT
66 CAAATAAATTTCGATTCGATTAACGGTCAAATAATTTCGATTCGATTAACGGTT
* *
115814 AAAT-AATTTCGGTTCGATTAATGGTTAAAGAAAAAA-AATCGGTTGATTTGGTTCGGTTAATAA
1 AAATAAATTTCGGTTCGATTAACGGTTAAAGAAAAAATAAT---TT-ATTTGATTCGGTTAATAA
* * *
115877 TTTTCAAATAAATTTCGGTTCGATTAACTGTTAAATAA
62 TTTTCAAATAAATTTCGATTCGATTAACGGTCAAATAA
115915 AAATAATTTA
Statistics
Matches: 88, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
117 3 0.03
118 30 0.34
119 4 0.05
120 2 0.02
121 49 0.56
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.39
Consensus pattern (119 bp):
AAATAAATTTCGGTTCGATTAACGGTTAAAGAAAAAATAATTTATTTGATTCGGTTAATAATTTT
CAAATAAATTTCGATTCGATTAACGGTCAAATAATTTCGATTCGATTAACGGTT
Found at i:115984 original size:27 final size:27
Alignment explanation
Indices: 115954--116084 Score: 101
Period size: 26 Copynumber: 4.9 Consensus size: 27
115944 TTAATAATTT
*
115954 TCAAATAAATTTGGGTTCGATTAACGG
1 TCAAATAAATTTCGGTTCGATTAACGG
* * *
115981 TCAAAT-AATTTTGGTTCGATTAATGTT
1 TCAAATAAATTTCGGTTCGATTAACG-G
* * * ***
116008 TAAAGAAAAAAATTT-GGTT--AATAAATT
1 T---CAAATAAATTTCGGTTCGATTAACGG
116035 TCAAATAAATTTCGGTTCGATTAACGG
1 TCAAATAAATTTCGGTTCGATTAACGG
116062 TCAAAT-AATTTCGGTTCGATTAA
1 TCAAATAAATTTCGGTTCGATTAA
116085 TGTTAAAGAA
Statistics
Matches: 82, Mismatches: 14, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
24 9 0.11
25 4 0.05
26 34 0.41
27 19 0.23
28 4 0.05
30 7 0.09
31 5 0.06
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.37
Consensus pattern (27 bp):
TCAAATAAATTTCGGTTCGATTAACGG
Found at i:115991 original size:195 final size:187
Alignment explanation
Indices: 115657--116003 Score: 487
Period size: 195 Copynumber: 1.8 Consensus size: 187
115647 TGTTAATGAT
115657 AAAAAAAATCGGTTAATTCAATTCGGTAAACAATTTTCAAATAAATTTCGGTTCGATTAACGGTT
1 AAAAAAAATCGGTTAATTCAATTCGGTAAACAATTTTCAAATAAATTTCGGTTCGATTAACGGTT
* * *
115722 AAGGAAAAAATAATTTATTTTATTTGGTTAATAATTTTCAAATAAATTTCGATTTGATTAACGGT
66 AAGAAAAAAATAATTTATTTTATTCGGTTAATAATTTTCAAATAAATTTCGATTCGATTAACGGT
115787 CAAATAATTTCGATTCGATTAACGGTTAAATAATTTCGGTTCGATTAATGGTTAAAG
131 CAAATAATTTCGATTCGATTAACGGTTAAATAATTTCGGTTCGATTAATGGTTAAAG
* *** * * *
115844 AAAAAAAATCGGTTGATTTGGTTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACTGTT
1 AAAAAAAATCGGTTAATTCAATTCGGTAAACAATTTTCAAATAAATTTCGGTTCGATTAACGGTT
* * *
115909 AAATAAAAATAATTTAATTTATTTGGTTAATTCGGTTAATAATTTTCAAATAAATTTGGGTTCGA
66 -AAGAAAAA-AA--TAATTTA-TT--TT-ATTCGGTTAATAATTTTCAAATAAATTTCGATTCGA
* *
115974 TTAACGGTCAAATAATTTTGGTTCGATTAA
123 TTAACGGTCAAATAATTTCGATTCGATTAA
116004 TGTTTAAAGA
Statistics
Matches: 137, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
187 58 0.42
188 6 0.04
189 2 0.01
191 7 0.05
192 2 0.01
194 2 0.01
195 60 0.44
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.39
Consensus pattern (187 bp):
AAAAAAAATCGGTTAATTCAATTCGGTAAACAATTTTCAAATAAATTTCGGTTCGATTAACGGTT
AAGAAAAAAATAATTTATTTTATTCGGTTAATAATTTTCAAATAAATTTCGATTCGATTAACGGT
CAAATAATTTCGATTCGATTAACGGTTAAATAATTTCGGTTCGATTAATGGTTAAAG
Found at i:116037 original size:81 final size:80
Alignment explanation
Indices: 115937--116109 Score: 301
Period size: 81 Copynumber: 2.1 Consensus size: 80
115927 TTATTTGGTT
* * *
115937 AATTCGGTTAATAATTTTCAAATAAATTTGGGTTCGATTAACGGTCAAATAATTTTGGTTCGATT
1 AATTCGGTTAATAAATTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATT
116002 AATGTTTAAAGAAAAA
66 AATG-TTAAAGAAAAA
*
116018 AATTTGGTTAATAAATTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATT
1 AATTCGGTTAATAAATTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATT
116083 AATGTTAAAGAAAAA
66 AATGTTAAAGAAAAA
116098 AATTCGGTTAAT
1 AATTCGGTTAAT
116110 TTGTTTTGGT
Statistics
Matches: 87, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
80 22 0.25
81 65 0.75
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.38
Consensus pattern (80 bp):
AATTCGGTTAATAAATTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATT
AATGTTAAAGAAAAA
Found at i:116131 original size:94 final size:94
Alignment explanation
Indices: 116020--116250 Score: 381
Period size: 94 Copynumber: 2.5 Consensus size: 94
116010 AAGAAAAAAA
*
116020 TTTGGTTAATAAATTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATTAA
1 TTTGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATTAA
*
116085 TGTTAAAGAAAAAAATTCGGTTAATTTGT
66 TGTTAAAGAAAAAAATTCGGTTAATTTGG
* * * *
116114 TTTGGTTAATAATTTTCAAATAATTTTTGGTTTGATTAACGATCAAATAATTTCGGTTCGATTAA
1 TTTGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATTAA
* *
116179 TGTTAAAGAAAAAATTTTGGTTAATTTGG
66 TGTTAAAGAAAAAAATTCGGTTAATTTGG
*
116208 TTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGT
1 TTTGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGT
116251 TAAAGAAAAA
Statistics
Matches: 124, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
94 124 1.00
ACGTcount: A:0.34, C:0.08, G:0.16, T:0.42
Consensus pattern (94 bp):
TTTGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATTAA
TGTTAAAGAAAAAAATTCGGTTAATTTGG
Found at i:116162 original size:175 final size:180
Alignment explanation
Indices: 115880--116203 Score: 489
Period size: 175 Copynumber: 1.8 Consensus size: 180
115870 TTAATAATTT
* * *
115880 TCAAATAAATTTCGGTTCGATTAACTGTTAAATAAAAATAATTTAATTTATTTGGTTAATTCGGT
1 TCAAATAAATTTCGGTTCGATTAACTGTTAAAGAAAAATAATTCAATTAATTTGGTT-ATTCGGT
* *
115945 TAATAATTTTCAAATAAATTTGGGTTCGATTAACGGTCAAATAATTTTGGTTCGATTAATGTTTA
65 TAATAATTTTCAAATAAATTTGGGTTCGATTAACGATCAAATAATTTCGGTTCGATTAATG-TTA
116010 AAGAAAAAAATTTGGTTAATAAATTTCAAATAAATTTCGGTTCGATTAACGG
129 AAGAAAAAAATTTGGTTAATAAATTTCAAATAAATTTCGGTTCGATTAACGG
**
116062 TCAAAT-AATTTCGGTTCGATTAA-TGTTAAAGAAAAA-AATTCGGTTAATTT-GTT-TT-GGTT
1 TCAAATAAATTTCGGTTCGATTAACTGTTAAAGAAAAATAATTCAATTAATTTGGTTATTCGGTT
* * *
116121 AATAATTTTCAAATAATTTTTGGTTTGATTAACGATCAAATAATTTCGGTTCGATTAATGTTAAA
66 AATAATTTTCAAATAAATTTGGGTTCGATTAACGATCAAATAATTTCGGTTCGATTAATGTTAAA
*
116186 GAAAAAATTTTGGTTAAT
131 GAAAAAAATTTGGTTAAT
116204 TTGGTTCGGT
Statistics
Matches: 131, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
174 22 0.17
175 59 0.45
176 2 0.02
178 3 0.02
179 10 0.08
180 12 0.09
181 17 0.13
182 6 0.05
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (180 bp):
TCAAATAAATTTCGGTTCGATTAACTGTTAAAGAAAAATAATTCAATTAATTTGGTTATTCGGTT
AATAATTTTCAAATAAATTTGGGTTCGATTAACGATCAAATAATTTCGGTTCGATTAATGTTAAA
GAAAAAAATTTGGTTAATAAATTTCAAATAAATTTCGGTTCGATTAACGG
Found at i:116575 original size:30 final size:30
Alignment explanation
Indices: 116540--116596 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
116530 ATAATATGTA
*
116540 AATATTAAGGACCAAATGTATAATTATTCT
1 AATATTAAGGACCAAATATATAATTATTCT
116570 AATATTAAGGACCAAATATATAATTAT
1 AATATTAAGGACCAAATATATAATTAT
116597 GCCAATTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.35
Consensus pattern (30 bp):
AATATTAAGGACCAAATATATAATTATTCT
Found at i:122413 original size:3 final size:3
Alignment explanation
Indices: 122407--122437 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
122397 ATAAAAAAAC
122407 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
122438 ACTCGCCCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:123865 original size:14 final size:14
Alignment explanation
Indices: 123846--123875 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
123836 ATAGAAACTT
123846 GAATAACTCGACTC
1 GAATAACTCGACTC
*
123860 GAATAACTCTACTC
1 GAATAACTCGACTC
123874 GA
1 GA
123876 TTCAAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.27, G:0.13, T:0.23
Consensus pattern (14 bp):
GAATAACTCGACTC
Found at i:126553 original size:31 final size:32
Alignment explanation
Indices: 126498--126557 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
126488 CTAAGGTAAA
***
126498 CCTTGGGTAGGCTCTCAGGCCCCAAGGTACTC
1 CCTTGGGTAGGCTCTCAAAACCCAAGGTACTC
126530 CCTTGGGTAGGCTCT-AAAACCCAAGGTA
1 CCTTGGGTAGGCTCTCAAAACCCAAGGTA
126558 TTCTTTAGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 10 0.40
32 15 0.60
ACGTcount: A:0.22, C:0.30, G:0.27, T:0.22
Consensus pattern (32 bp):
CCTTGGGTAGGCTCTCAAAACCCAAGGTACTC
Found at i:126584 original size:31 final size:31
Alignment explanation
Indices: 126498--126592 Score: 93
Period size: 31 Copynumber: 3.1 Consensus size: 31
126488 CTAAGGTAAA
* * *
126498 CCTTGGGTAGGCTCTCAGGCCCCAAGGTACTC
1 CCTTAGGTAGGCTCTAAGGCCCCAAGGTA-TT
* **
126530 CCTTGGGTAGGCTCTAA-AACCCAAGGTATT
1 CCTTAGGTAGGCTCTAAGGCCCCAAGGTATT
* * *
126560 CTTTAGGTATGCTCTAAGGCCCCAAGGCATT
1 CCTTAGGTAGGCTCTAAGGCCCCAAGGTATT
126591 CC
1 CC
126593 CTTATATTGG
Statistics
Matches: 51, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
30 15 0.29
31 20 0.39
32 16 0.31
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.25
Consensus pattern (31 bp):
CCTTAGGTAGGCTCTAAGGCCCCAAGGTATT
Found at i:129031 original size:13 final size:13
Alignment explanation
Indices: 129013--129037 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
129003 GGGTCTTCAC
129013 TTGTAAATGGGCT
1 TTGTAAATGGGCT
129026 TTGTAAATGGGC
1 TTGTAAATGGGC
129038 CTCCGATTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.32, T:0.36
Consensus pattern (13 bp):
TTGTAAATGGGCT
Found at i:129688 original size:25 final size:26
Alignment explanation
Indices: 129619--129688 Score: 74
Period size: 28 Copynumber: 2.7 Consensus size: 26
129609 ATAAACAAAT
*
129619 AAATAAATAAAAT-AAGAAGAAAATAC
1 AAATAAA-AAAATGAAGAAGAAAATAA
129645 AAATAAAAAAATGTAAAGAAGATAAA-AA
1 AAATAAAAAAATG--AAGAAGA-AAATAA
129673 AAAT-AAAAAATGAAGA
1 AAATAAAAAAATGAAGA
129689 TAAGTAATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
25 9 0.23
26 7 0.18
27 8 0.21
28 12 0.31
29 3 0.08
ACGTcount: A:0.74, C:0.01, G:0.10, T:0.14
Consensus pattern (26 bp):
AAATAAAAAAATGAAGAAGAAAATAA
Found at i:129758 original size:3 final size:3
Alignment explanation
Indices: 129752--129786 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
129742 AATAAAATAG
129752 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
129787 AAACAGTAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:129848 original size:29 final size:30
Alignment explanation
Indices: 129814--129876 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 30
129804 TAATAAAATA
129814 AAATAAAAATAGAAGGATATAAG-AATAAT
1 AAATAAAAATAGAAGGATATAAGTAATAAT
* * * *
129843 AAAT-AAAATATATGTATATATGTAATAAT
1 AAATAAAAATAGAAGGATATAAGTAATAAT
129872 AAATA
1 AAATA
129877 TAATATTTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
28 14 0.50
29 14 0.50
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.29
Consensus pattern (30 bp):
AAATAAAAATAGAAGGATATAAGTAATAAT
Found at i:130549 original size:37 final size:37
Alignment explanation
Indices: 130499--130610 Score: 156
Period size: 37 Copynumber: 3.0 Consensus size: 37
130489 ATGCTTATAG
130499 ATCCTATTTTTAGGAGTTTGAACCATAGTAAAA-TGCT
1 ATCCTATTTTTAGGAGTTTGAACCATAGTAAAACT-CT
* *
130536 ATCCTATTTTTAGGAGTTTGAATCATAATAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAACCATAGTAAAACTCT
* *
130573 ATCATAATTTTAGGAGTTTGAATCC-TAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAA-CCATAGTAAAACTCT
130610 A
1 A
130611 ACGTTATGTT
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
37 65 0.97
38 2 0.03
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.38
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAACCATAGTAAAACTCT
Found at i:133492 original size:14 final size:14
Alignment explanation
Indices: 133473--133500 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
133463 CGTTCATGAA
133473 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
133487 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
133501 TGTTTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.14, G:0.29, T:0.50
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:134663 original size:16 final size:16
Alignment explanation
Indices: 134638--134710 Score: 87
Period size: 16 Copynumber: 4.7 Consensus size: 16
134628 CCAACGTTTA
* *
134638 TGTTCGTTTATATTCG
1 TGTTCATTTATGTTCG
134654 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
* *
134670 TGTTCGTTTATGTTTG
1 TGTTCATTTATGTTCG
*
134686 TGTTCTTTTATGTTCG
1 TGTTCATTTATGTTCG
134702 T-TT-ATTTAT
1 TGTTCATTTAT
134711 TAAATGAACG
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
14 5 0.10
15 2 0.04
16 43 0.86
ACGTcount: A:0.11, C:0.10, G:0.18, T:0.62
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:134679 original size:32 final size:32
Alignment explanation
Indices: 134638--134702 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
134628 CCAACGTTTA
134638 TGTTCGTTTATATTCGTGTTCATTTATGTTCG
1 TGTTCGTTTATATTCGTGTTCATTTATGTTCG
* * *
134670 TGTTCGTTTATGTTTGTGTTCTTTTATGTTCG
1 TGTTCGTTTATATTCGTGTTCATTTATGTTCG
134702 T
1 T
134703 TTATTTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.09, C:0.11, G:0.20, T:0.60
Consensus pattern (32 bp):
TGTTCGTTTATATTCGTGTTCATTTATGTTCG
Found at i:135688 original size:2 final size:2
Alignment explanation
Indices: 135681--135719 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
135671 GATAGTTTTA
135681 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
135720 AAATTAAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:143099 original size:31 final size:31
Alignment explanation
Indices: 143040--143099 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
143030 ACTTACCACA
*
143040 AATACTAATTTAAACCAAAATATGAAATTTT
1 AATACTAATTTAAACCAAAATATCAAATTTT
*
143071 AATACTAATTTAAATCAACAA-ATCAAATT
1 AATACTAATTTAAACCAA-AATATCAAATT
143100 CAAGACATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.53, C:0.12, G:0.02, T:0.33
Consensus pattern (31 bp):
AATACTAATTTAAACCAAAATATCAAATTTT
Found at i:148845 original size:397 final size:397
Alignment explanation
Indices: 148112--148908 Score: 1576
Period size: 397 Copynumber: 2.0 Consensus size: 397
148102 CCTTGCCTAA
*
148112 ATCCTTAAAATCATTGAGAGGATTTTTGGGATTGACATGCTGTTATAGAAGCTTTATCAGAGATT
1 ATCCTTAAAATCATTGAGAGGATTTTTGGGATTGACATGCTATTATAGAAGCTTTATCAGAGATT
148177 ATGCTGATATTAGTAAACCTTTGAATCAGTTGTTAAAGAAGGACTGTTTTAAGTGGAACAGTGCA
66 ATGCTGATATTAGTAAACCTTTGAATCAGTTGTTAAAGAAGGACTGTTTTAAGTGGAACAGTGCA
148242 GCTTTGACTGCTTTTGAAGAGCTTAAGAAAACTATGTGTCTTGCACCTGTTCTAGCCCTACCAGA
131 GCTTTGACTGCTTTTGAAGAGCTTAAGAAAACTATGTGTCTTGCACCTGTTCTAGCCCTACCAGA
*
148307 CTTTACTAAAAGTTTTTATTTGGAAACTGATGCCAGCTCTGGAAGCATAGGGGTTGTTTTATCTC
196 CTTTACTAAAAGTTTTTATTTGGAAACTAATGCCAGCTCTGGAAGCATAGGGGTTGTTTTATCTC
148372 AAGATGGCAGACCTATAGCATTTCTAAGTAAAGCTCTCAGTCCAAGACATGCTGCTCTATCTATT
261 AAGATGGCAGACCTATAGCATTTCTAAGTAAAGCTCTCAGTCCAAGACATGCTGCTCTATCTATT
148437 TATGAGAGGGAATACCTTGCTATTTTATTAGCAGTTTCCAAATTGAGACACTATTTGGAAAGCAA
326 TATGAGAGGGAATACCTTGCTATTTTATTAGCAGTTTCCAAATTGAGACACTATTTGGAAAGCAA
148502 GCCTTTT
391 GCCTTTT
148509 ATCCTTAAAATCATTGAGAGGATTTTTGGGATTGACATGCTATTATAGAAGCTTTATCAGAGATT
1 ATCCTTAAAATCATTGAGAGGATTTTTGGGATTGACATGCTATTATAGAAGCTTTATCAGAGATT
148574 ATGCTGATATTAGTAAACCTTTGAATCAGTTGTTAAAGAAGGACTGTTTTAAGTGGAACAGTGCA
66 ATGCTGATATTAGTAAACCTTTGAATCAGTTGTTAAAGAAGGACTGTTTTAAGTGGAACAGTGCA
148639 GCTTTGACTGCTTTTGAAGAGCTTAAGAAAACTATGTGTCTTGCACCTGTTCTAGCCCTACCAGA
131 GCTTTGACTGCTTTTGAAGAGCTTAAGAAAACTATGTGTCTTGCACCTGTTCTAGCCCTACCAGA
148704 CTTTACTAAAAGTTTTTATTTGGAAACTAATGCCAGCTCTGGAAGCATAGGGGTTGTTTTATCTC
196 CTTTACTAAAAGTTTTTATTTGGAAACTAATGCCAGCTCTGGAAGCATAGGGGTTGTTTTATCTC
148769 AAGATGGCAGACCTATAGCATTTCTAAGTAAAGCTCTCAGTCCAAGACATGCTGCTCTATCTATT
261 AAGATGGCAGACCTATAGCATTTCTAAGTAAAGCTCTCAGTCCAAGACATGCTGCTCTATCTATT
148834 TATGAGAGGGAATACCTTGCTATTTTATTAGCAGTTTCCAAATTGAGACACTATTTGGAAAGCAA
326 TATGAGAGGGAATACCTTGCTATTTTATTAGCAGTTTCCAAATTGAGACACTATTTGGAAAGCAA
148899 GCCTTTT
391 GCCTTTT
148906 ATC
1 ATC
148909 ATCAAAATTG
Statistics
Matches: 398, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
397 398 1.00
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.34
Consensus pattern (397 bp):
ATCCTTAAAATCATTGAGAGGATTTTTGGGATTGACATGCTATTATAGAAGCTTTATCAGAGATT
ATGCTGATATTAGTAAACCTTTGAATCAGTTGTTAAAGAAGGACTGTTTTAAGTGGAACAGTGCA
GCTTTGACTGCTTTTGAAGAGCTTAAGAAAACTATGTGTCTTGCACCTGTTCTAGCCCTACCAGA
CTTTACTAAAAGTTTTTATTTGGAAACTAATGCCAGCTCTGGAAGCATAGGGGTTGTTTTATCTC
AAGATGGCAGACCTATAGCATTTCTAAGTAAAGCTCTCAGTCCAAGACATGCTGCTCTATCTATT
TATGAGAGGGAATACCTTGCTATTTTATTAGCAGTTTCCAAATTGAGACACTATTTGGAAAGCAA
GCCTTTT
Found at i:167814 original size:12 final size:12
Alignment explanation
Indices: 167792--167835 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
167782 TATTATATGG
167792 CATGAACAATAC
1 CATGAACAATAC
* *
167804 CGTGAATAATAC
1 CATGAACAATAC
* *
167816 CATGAACAGTAT
1 CATGAACAATAC
167828 CATGAACA
1 CATGAACA
167836 GTGAAAAATT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.45, C:0.20, G:0.14, T:0.20
Consensus pattern (12 bp):
CATGAACAATAC
Found at i:168526 original size:24 final size:24
Alignment explanation
Indices: 168499--168566 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 24
168489 CACCACAGCT
*
168499 CGTATAAATTGCACCGAAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
* * * *
168523 CGTAGAATTTGTACCGAAGTGTCG
1 CGTAGAAATTGCACCGAAGTGCCA
*
168547 CGTAGAAA-TGCACCGTAGTG
1 CGTAGAAATTGCACCGAAGTG
168567 TCATATAAGA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
23 10 0.28
24 26 0.72
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (24 bp):
CGTAGAAATTGCACCGAAGTGCCA
Found at i:182406 original size:25 final size:27
Alignment explanation
Indices: 182374--182434 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
182364 TATTATGTAT
182374 TTATATAATT-TTATT-TA-ATCTAATA
1 TTATATAATTCTTATTATAGAT-TAATA
*
182399 TTATATAATTCTTTTTGATAGATTAATA
1 TTATATAATTCTTATT-ATAGATTAATA
182427 TTATATAA
1 TTATATAA
182435 ATTATAACAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
25 10 0.32
26 4 0.13
28 15 0.48
29 2 0.06
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.54
Consensus pattern (27 bp):
TTATATAATTCTTATTATAGATTAATA
Found at i:184084 original size:37 final size:39
Alignment explanation
Indices: 184006--184085 Score: 103
Period size: 38 Copynumber: 2.1 Consensus size: 39
183996 AACAAGTTGG
* *
184006 AAAATATTTATATATTTTCTTTAAAAAATTTAAATTCAT
1 AAAATATTTATATATTTTCTTTAAAAAATTGAAAATCAT
*
184045 AAAAT-TTATATATATTTT-TTTATAAAATTGAAAAT-AT
1 AAAATATT-TATATATTTTCTTTAAAAAATTGAAAATCAT
184082 AAAA
1 AAAA
184086 AAGTTGAATG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
37 6 0.16
38 16 0.43
39 15 0.41
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (39 bp):
AAAATATTTATATATTTTCTTTAAAAAATTGAAAATCAT
Found at i:185653 original size:12 final size:12
Alignment explanation
Indices: 185636--185661 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
185626 ATACCTAACG
185636 TTTATTTTTTAT
1 TTTATTTTTTAT
185648 TTTATTTTTTAT
1 TTTATTTTTTAT
185660 TT
1 TT
185662 AGTACTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTATTTTTTAT
Found at i:185908 original size:9 final size:9
Alignment explanation
Indices: 185894--185919 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
185884 AAGTTTAAAT
185894 ACTAAAACG
1 ACTAAAACG
185903 ACTAAAACG
1 ACTAAAACG
185912 ACTAAAAC
1 ACTAAAAC
185920 TGATAGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.23, G:0.08, T:0.12
Consensus pattern (9 bp):
ACTAAAACG
Found at i:187266 original size:4 final size:4
Alignment explanation
Indices: 187257--187335 Score: 52
Period size: 4 Copynumber: 18.0 Consensus size: 4
187247 AAATTTTTCA
* *
187257 ATTT ATTT ATTT ATTT ATTC ATTT ATTT CGAACTT ATGCTT -TTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ---ATTT AT--TT ATTT ATTT
*
187305 ATTT ATTT AGTT ATTT CAAATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ---ATTT ATTT ATTT
187336 GTTTGTTTCA
Statistics
Matches: 60, Mismatches: 6, Indels: 18
0.71 0.07 0.21
Matches are distributed among these distances:
3 2 0.03
4 48 0.80
5 1 0.02
6 2 0.03
7 7 0.12
ACGTcount: A:0.25, C:0.06, G:0.04, T:0.65
Consensus pattern (4 bp):
ATTT
Found at i:187363 original size:23 final size:23
Alignment explanation
Indices: 187303--187363 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
187293 TGCTTTTTAT
* * *
187303 TTATTTATTTAGTTATTTCAAAT
1 TTATTTATTTATTTGTTTCAAAA
*
187326 TTATTTATTTGTTTGTTTCAAAA
1 TTATTTATTTATTTGTTTCAAAA
*
187349 TTATTTGTTTATTTG
1 TTATTTATTTATTTG
187364 AAGAGATATG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.25, C:0.03, G:0.08, T:0.64
Consensus pattern (23 bp):
TTATTTATTTATTTGTTTCAAAA
Found at i:188227 original size:19 final size:20
Alignment explanation
Indices: 188189--188228 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
188179 GAAACCCCTT
*
188189 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
188209 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
188228 T
1 T
188229 AAAGATAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.38
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:205126 original size:2 final size:2
Alignment explanation
Indices: 205119--205146 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
205109 TTCCTAAACC
205119 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
205147 TCTTTCCTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:210393 original size:20 final size:20
Alignment explanation
Indices: 210368--210405 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
210358 TAATTGAAAA
210368 TAATTATAATAATATTTTTT
1 TAATTATAATAATATTTTTT
* *
210388 TAATTATGATATTATTTT
1 TAATTATAATAATATTTT
210406 ATCAAATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (20 bp):
TAATTATAATAATATTTTTT
Found at i:218441 original size:21 final size:20
Alignment explanation
Indices: 218415--218484 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
218405 TATTCTTTTT
218415 TAAAAATTAATAAAAATGCAA
1 TAAAAATTAATAAAAATG-AA
* *
218436 TAAAAAATAATTAAAAGTGAA
1 TAAAAATTAA-TAAAAATGAA
*
218457 T-AAAATTCAATAAAAAAGAA
1 TAAAAATT-AATAAAAATGAA
*
218477 TATAAATT
1 TAAAAATT
218485 TAAAAAATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
20 14 0.35
21 19 0.47
22 7 0.17
ACGTcount: A:0.66, C:0.03, G:0.06, T:0.26
Consensus pattern (20 bp):
TAAAAATTAATAAAAATGAA
Found at i:218478 original size:10 final size:10
Alignment explanation
Indices: 218415--218483 Score: 50
Period size: 10 Copynumber: 6.7 Consensus size: 10
218405 TATTCTTTTT
*
218415 TAAAAATTAA
1 TAAAAATGAA
218425 TAAAAATGCAA
1 TAAAAATG-AA
218436 TAAAAAAT-AA
1 T-AAAAATGAA
*
218446 TTAAAAGTGAA
1 -TAAAAATGAA
* *
218457 TAAAATTCAA
1 TAAAAATGAA
*
218467 TAAAAAAGAA
1 TAAAAATGAA
*
218477 TATAAAT
1 TAAAAAT
218484 TTAAAAAATA
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
10 34 0.74
11 6 0.13
12 6 0.13
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (10 bp):
TAAAAATGAA
Found at i:219370 original size:13 final size:14
Alignment explanation
Indices: 219352--219385 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
219342 AAAATAAATT
219352 ATATTTTAT-GAAA
1 ATATTTTATGGAAA
219365 ATATTTT-TGGAAA
1 ATATTTTATGGAAA
219378 ATATTTTA
1 ATATTTTA
219386 CGGTATTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 1 0.05
13 18 0.95
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (14 bp):
ATATTTTATGGAAA
Found at i:219662 original size:42 final size:42
Alignment explanation
Indices: 219615--219745 Score: 135
Period size: 42 Copynumber: 3.2 Consensus size: 42
219605 AAAATATAGT
219615 TATTATAAATTATAGTAATTAATTATTAAAATAAGAATAATA
1 TATTATAAATTATAGTAATTAATTATTAAAATAAGAATAATA
* * * *
219657 TATTATTAATTATATTAATTATTTATTAAAATAATAAT-AT-
1 TATTATAAATTATAGTAATTAATTATTAAAATAAGAATAATA
* * * * *
219697 TGTTA-AAA-TATTGAAAATTATAATATTAAAATAAGAATATTA
1 TATTATAAATTATAG-TAATTA-ATTATTAAAATAAGAATAATA
219739 TATTATA
1 TATTATA
219746 TTTTAAGGAG
Statistics
Matches: 70, Mismatches: 14, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
38 3 0.04
39 7 0.10
40 18 0.26
41 3 0.04
42 38 0.54
43 1 0.01
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (42 bp):
TATTATAAATTATAGTAATTAATTATTAAAATAAGAATAATA
Found at i:219669 original size:82 final size:82
Alignment explanation
Indices: 219583--219744 Score: 188
Period size: 82 Copynumber: 2.0 Consensus size: 82
219573 TAAATAAAAT
* * * *
219583 ATTATGATCAATATATTTTATTAAAAT-ATAGTTATT-ATAAATTATAG-TAATTA-ATTATTAA
1 ATTAT-ATCAAT-TA-TTTATTAAAATAATA-ATATTGATAAAATATAGAAAATTATAATATTAA
219644 AATAAGAATAATATATTATTA
62 AATAAGAATAATATATTATTA
* * *
219665 ATTATATTAATTATTTATTAAAATAATAATATTGTTAAAATATTGAAAATTATAATATTAAAATA
1 ATTATATCAATTATTTATTAAAATAATAATATTGATAAAATATAGAAAATTATAATATTAAAATA
*
219730 AGAATATTATATTAT
66 AGAATAATATATTAT
219745 ATTTTAAGGA
Statistics
Matches: 68, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
79 15 0.22
80 13 0.19
81 10 0.15
82 30 0.44
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.45
Consensus pattern (82 bp):
ATTATATCAATTATTTATTAAAATAATAATATTGATAAAATATAGAAAATTATAATATTAAAATA
AGAATAATATATTATTA
Found at i:219878 original size:14 final size:15
Alignment explanation
Indices: 219861--219934 Score: 59
Period size: 14 Copynumber: 5.1 Consensus size: 15
219851 AGTATAATTT
219861 TATATATT-TAATAA
1 TATATATTATAATAA
219875 TATA-ATTATAATAA
1 TATATATTATAATAA
* *
219889 TATTATATTATATTAT
1 TA-TATATTATAATAA
*
219905 TA-AAATTATCAATAA
1 TATATATTAT-AATAA
219920 -ATATAATT-TAATAA
1 TATAT-ATTATAATAA
219934 T
1 T
219935 TAATATTTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
13 3 0.06
14 24 0.51
15 7 0.15
16 13 0.28
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (15 bp):
TATATATTATAATAA
Found at i:219968 original size:45 final size:47
Alignment explanation
Indices: 219870--219969 Score: 129
Period size: 42 Copynumber: 2.2 Consensus size: 47
219860 TTATATATTT
*
219870 AATAATATAATTATAATAATATTATATTATATTATTAAAATTATCAA
1 AATAATATAATTATAATAATATAATATTATATTATTAAAATTATCAA
*
219917 TA-AATATAATT-TAATAAT-TAATATT-T-TTATTAAAATTATACTAA
1 AATAATATAATTATAATAATATAATATTATATTATTAAAATTAT-C-AA
219961 AATAATATA
1 AATAATATA
219970 TTGATATTCA
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
42 13 0.28
43 2 0.04
44 9 0.19
45 13 0.28
46 9 0.19
47 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (47 bp):
AATAATATAATTATAATAATATAATATTATATTATTAAAATTATCAA
Found at i:220750 original size:11 final size:11
Alignment explanation
Indices: 220734--220817 Score: 57
Period size: 11 Copynumber: 7.2 Consensus size: 11
220724 CGCTACATAA
220734 TATTTTTTTGT
1 TATTTTTTTGT
*
220745 TATTTTTCTGAT
1 TATTTTTTTG-T
220757 T-TTTGGTTTTCGT
1 TATTT--TTTT-GT
220770 TATTTTTTT-T
1 TATTTTTTTGT
220780 TACTTTTTTTTGT
1 TA--TTTTTTTGT
220793 TATTTTCTTT-T
1 TATTTT-TTTGT
*
220804 TCTTTTCTTTGT
1 TATTTT-TTTGT
220816 TA
1 TA
220818 CATTATTTTC
Statistics
Matches: 59, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
10 3 0.05
11 26 0.44
12 18 0.31
13 8 0.14
14 4 0.07
ACGTcount: A:0.08, C:0.07, G:0.08, T:0.76
Consensus pattern (11 bp):
TATTTTTTTGT
Found at i:220794 original size:23 final size:23
Alignment explanation
Indices: 220736--220817 Score: 78
Period size: 23 Copynumber: 3.5 Consensus size: 23
220726 CTACATAATA
* * *
220736 TTTTTTTGTTA-TTTTTCTGATT
1 TTTTTTTGTTATTTTTTTTTACT
220758 TTTGGTTTTCGTTATTTTTTTTTACT
1 TTT--TTTT-GTTATTTTTTTTTACT
220784 TTTTTTTGTTATTTTCTTTTT-CT
1 TTTTTTTGTTATTTT-TTTTTACT
*
220807 TTTCTTTGTTA
1 TTTTTTTGTTA
220818 CATTATTTTC
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
22 3 0.06
23 20 0.39
24 13 0.25
25 4 0.08
26 11 0.22
ACGTcount: A:0.07, C:0.07, G:0.09, T:0.77
Consensus pattern (23 bp):
TTTTTTTGTTATTTTTTTTTACT
Found at i:220826 original size:23 final size:23
Alignment explanation
Indices: 220776--220836 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 23
220766 TCGTTATTTT
* ** *
220776 TTTTTACTTTTTTTTGTTATTTTC
1 TTTTT-CTTTTCTTTGTTACATTA
220800 TTTTTCTTTTCTTTGTTACATTA
1 TTTTTCTTTTCTTTGTTACATTA
220823 TTTTCTCTTATTCT
1 TTTT-TCTT-TTCT
220837 ATCTTTTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 18 0.58
24 9 0.29
25 4 0.13
ACGTcount: A:0.10, C:0.13, G:0.03, T:0.74
Consensus pattern (23 bp):
TTTTTCTTTTCTTTGTTACATTA
Found at i:229429 original size:30 final size:31
Alignment explanation
Indices: 229370--229431 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
229360 ACTAATAGTT
* * * *
229370 TATCTAAAGTTTTAGGGTTAAATTAGTATTC
1 TATCTAAAGTTTTAAGATCAAACTAGTATTC
229401 TATCTAAAG-TTTAAGATCAAACTAGTATTC
1 TATCTAAAGTTTTAAGATCAAACTAGTATTC
229431 T
1 T
229432 GTTAAAATTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 18 0.67
31 9 0.33
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (31 bp):
TATCTAAAGTTTTAAGATCAAACTAGTATTC
Found at i:237050 original size:20 final size:20
Alignment explanation
Indices: 237025--237068 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
237015 CGTTTCACTT
237025 ATCCTCCATTGGAGTACAAA
1 ATCCTCCATTGGAGTACAAA
237045 ATCCTCCATTGGAGTACAAA
1 ATCCTCCATTGGAGTACAAA
237065 ATCC
1 ATCC
237069 AGGGTATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.25
Consensus pattern (20 bp):
ATCCTCCATTGGAGTACAAA
Found at i:240882 original size:55 final size:55
Alignment explanation
Indices: 240221--240868 Score: 1035
Period size: 55 Copynumber: 11.8 Consensus size: 55
240211 TAGTGTGCAA
240221 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* * * *
240276 AAACTTGAGAAATTCATATTAAGTGGATGAATTTCTGTATGGGCACTATATATGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* * * *
240331 AAACTTAAGAAATTCATAATAAGTAGATGAATTTTCGTATGGACACTATATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* *
240386 AAACTTAAGAAATCCATACTAAGTGGATGAATTTCCGTATGGACACTATATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* *
240441 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGTACTATATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
240496 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* *
240551 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATTGACACTATATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* *
240606 AAACTTAACAAATTCATACTCAGTGGATGAATTTCCGTATGGGCACTATATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* *
240661 TAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTGTATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
** **
240716 AAACTTAAGAAATTCATACTAAGTGGATGAATTTATGTATGGGCGTTATATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
** *
240771 AAACTTAAGAAATTCATACTAAGTGGATGAATTTATGTATGGGCACTATATGTGC
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* * * *
240826 AAGCTTAAGAAATCCATACTAAGTGTATGAATTTCTGTATGGG
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGG
240869 AGATATATGT
Statistics
Matches: 549, Mismatches: 44, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 549 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (55 bp):
AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
Found at i:241162 original size:68 final size:68
Alignment explanation
Indices: 241078--241348 Score: 397
Period size: 68 Copynumber: 4.0 Consensus size: 68
241068 AAGATTAATA
* * *
241078 GCCTAACTGTGCATTTGACATAAATGTGTCAATTATGCCAGTTAGATAAAAGGCTAAGTGCCTTT
1 GCCTAACTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAATGCCTTT
241143 GAG
66 GAG
*
241146 GCCTAACTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
1 GCCTAACTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAATGCCTTT
241211 GAG
66 GAG
* *
241214 GCCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAATATAG--T
1 GCCTAACTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAA-AT-GCCT
241277 TT-AG
64 TTGAG
* * **
241281 GCCTAACTGTGCATTTGACAGAAA-GATTTCAATCATGCCAGTTAGATGAAAGATTAAATGCCTT
1 GCCTAACTGTGCATTTGACAGAAATG-TGTCAATTATGCCAGTTAGATGAAAGGCTAAATGCCTT
241345 TGAG
65 TGAG
241349 AAAAAGACTA
Statistics
Matches: 187, Mismatches: 10, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
65 1 0.01
66 3 0.02
67 55 0.29
68 126 0.67
69 1 0.01
70 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (68 bp):
GCCTAACTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAATGCCTTT
GAG
Found at i:241343 original size:135 final size:135
Alignment explanation
Indices: 241078--241348 Score: 395
Period size: 135 Copynumber: 2.0 Consensus size: 135
241068 AAGATTAATA
* * * *
241078 GCCTAACTGTGCATTTGACATAAATGTGTCAATTATGCCAGTTAGATAAAAGGCTAAGTGCCTTT
1 GCCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATAAAAGGCTAAATG-CTTT
* * *
241143 GAGGCCTAACTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
65 GAGGCCTAACTGTGCATTTGACAGAAATGTGTCAATCATGCCAGTTAGATGAAAGACTAAATGCC
241208 TTTGAG
130 TTTGAG
*
241214 GCCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAATATAG-TT
1 GCCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATAAAAGGCTAA-AT-GCTT
* *
241278 T-AGGCCTAACTGTGCATTTGACAGAAA-GATTTCAATCATGCCAGTTAGATGAAAGATTAAATG
64 TGAGGCCTAACTGTGCATTTGACAGAAATG-TGTCAATCATGCCAGTTAGATGAAAGACTAAATG
241341 CCTTTGAG
128 CCTTTGAG
241349 AAAAAGACTA
Statistics
Matches: 122, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
134 1 0.01
135 63 0.52
136 56 0.46
137 1 0.01
138 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (135 bp):
GCCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATAAAAGGCTAAATGCTTTG
AGGCCTAACTGTGCATTTGACAGAAATGTGTCAATCATGCCAGTTAGATGAAAGACTAAATGCCT
TTGAG
Found at i:241420 original size:45 final size:46
Alignment explanation
Indices: 241369--241507 Score: 196
Period size: 45 Copynumber: 3.1 Consensus size: 46
241359 GATGTATAAC
*
241369 AATGTATAAT-GTCGTATAAAAGGCATGAAAGGATGTCATAAATGA
1 AATGTATAATAGTCGTATAAAAGGCATGAAAGGATGCCATAAATGA
* *
241414 AATGTATAATAGT-GTA-AAAAGGGGCATGAAAGGATGCCCTAAATAA
1 AATGTATAATAGTCGTATAAAA--GGCATGAAAGGATGCCATAAATGA
*
241460 AATGCATAATAG-CGTATAAAAGGCATGAAAGGATGCCATAAATGA
1 AATGTATAATAGTCGTATAAAAGGCATGAAAGGATGCCATAAATGA
241505 AAT
1 AAT
241508 ACATAGGGGT
Statistics
Matches: 83, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
44 4 0.05
45 38 0.46
46 37 0.45
47 4 0.05
ACGTcount: A:0.46, C:0.09, G:0.22, T:0.23
Consensus pattern (46 bp):
AATGTATAATAGTCGTATAAAAGGCATGAAAGGATGCCATAAATGA
Found at i:241535 original size:45 final size:44
Alignment explanation
Indices: 241481--241568 Score: 122
Period size: 45 Copynumber: 2.0 Consensus size: 44
241471 GCGTATAAAA
*
241481 GGCATGAAAGGATGCCATAAATGAAATACATAGGGGTGCATTATC
1 GGCACGAAAGGATGCCATAAATGAAATACATA-GGGTGCATTATC
* * * *
241526 GGCACGAAAGGATGCCATAATTGAGATGCATATGGTGCATTAT
1 GGCACGAAAGGATGCCATAAATGAAATACATAGGGTGCATTAT
241569 AAATATGAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
44 10 0.26
45 28 0.74
ACGTcount: A:0.35, C:0.14, G:0.27, T:0.24
Consensus pattern (44 bp):
GGCACGAAAGGATGCCATAAATGAAATACATAGGGTGCATTATC
Found at i:242232 original size:88 final size:88
Alignment explanation
Indices: 242083--242258 Score: 343
Period size: 88 Copynumber: 2.0 Consensus size: 88
242073 AAATCTGGAA
242083 ACAAAATTTTACGGGTTTTTAGAAGAAGAAATATTTTAAAAGTGATGTGACATATGTATTTCGTA
1 ACAAAATTTTACGGGTTTTTAGAAGAAGAAATATTTTAAAAGTGATGTGACATATGTATTTCGTA
*
242148 TACGGAAGGGTACACGGAATATG
66 TACAGAAGGGTACACGGAATATG
242171 ACAAAATTTTACGGGTTTTTAGAAGAAGAAATATTTTAAAAGTGATGTGACATATGTATTTCGTA
1 ACAAAATTTTACGGGTTTTTAGAAGAAGAAATATTTTAAAAGTGATGTGACATATGTATTTCGTA
242236 TACAGAAGGGTACACGGAATATG
66 TACAGAAGGGTACACGGAATATG
242259 GTTGTTACAA
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 87 1.00
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.32
Consensus pattern (88 bp):
ACAAAATTTTACGGGTTTTTAGAAGAAGAAATATTTTAAAAGTGATGTGACATATGTATTTCGTA
TACAGAAGGGTACACGGAATATG
Found at i:242626 original size:7 final size:7
Alignment explanation
Indices: 242614--242658 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
242604 GTCATTACAA
242614 TAAACCC
1 TAAACCC
242621 TAAACCC
1 TAAACCC
*
242628 TAAA-CT
1 TAAACCC
* *
242634 TAAATCA
1 TAAACCC
242641 TAAACCC
1 TAAACCC
242648 TAAACCC
1 TAAACCC
242655 TAAA
1 TAAA
242659 TTGTACTTAC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
6 5 0.15
7 28 0.85
ACGTcount: A:0.49, C:0.31, G:0.00, T:0.20
Consensus pattern (7 bp):
TAAACCC
Found at i:247281 original size:16 final size:16
Alignment explanation
Indices: 247260--247298 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
247250 CATTGATTTA
247260 GCACCAATAATTCACT
1 GCACCAATAATTCACT
247276 GCACCAATAATTCACT
1 GCACCAATAATTCACT
247292 GCACCAA
1 GCACCAA
247299 CAGTGCTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.38, C:0.33, G:0.08, T:0.21
Consensus pattern (16 bp):
GCACCAATAATTCACT
Found at i:254134 original size:24 final size:23
Alignment explanation
Indices: 254098--254143 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
254088 ATAATCATTT
*
254098 AATAATTTATTATATATTTTTTGA
1 AATAATTTATTAT-TACTTTTTGA
*
254122 AATAATTTTTTATTACTTTTTG
1 AATAATTTATTATTACTTTTTG
254144 TAGTTATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (23 bp):
AATAATTTATTATTACTTTTTGA
Found at i:255101 original size:21 final size:19
Alignment explanation
Indices: 255044--255098 Score: 94
Period size: 19 Copynumber: 2.9 Consensus size: 19
255034 TATTGAGTTC
255044 GTATATAAATAATTTTTAA
1 GTATATAAATAATTTTTAA
255063 GTATATAAATAATTTTTAA
1 GTATATAAATAATTTTTAA
255082 GTATAT-AATGAATTTTT
1 GTATATAAAT-AATTTTT
255099 TTACACTGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
18 3 0.09
19 32 0.91
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (19 bp):
GTATATAAATAATTTTTAA
Found at i:258418 original size:26 final size:25
Alignment explanation
Indices: 258388--258452 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 25
258378 ATGCAAAAAG
258388 TAATAAAAAATTAATACAATAAAATA
1 TAATAAAAAATTAATA-AATAAAATA
** * *
258414 TAATAAACTATTAAATAATTATAATA
1 TAATAAAAAATT-AATAAATAAAATA
258440 TAATAAAAAATTA
1 TAATAAAAAATTA
258453 GCTTCTAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
25 1 0.03
26 27 0.84
27 4 0.12
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (25 bp):
TAATAAAAAATTAATAAATAAAATA
Found at i:260158 original size:30 final size:30
Alignment explanation
Indices: 260122--260186 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
260112 CTTCTATTAG
*
260122 TTCATAAAATAATAGAGCATCCCGTATCAA
1 TTCATAAAATAACAGAGCATCCCGTATCAA
* * *
260152 TTCATAAAATAACGGAGCATCTCGTATCAG
1 TTCATAAAATAACAGAGCATCCCGTATCAA
260182 TTCAT
1 TTCAT
260187 GATACATATG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.29
Consensus pattern (30 bp):
TTCATAAAATAACAGAGCATCCCGTATCAA
Found at i:261103 original size:31 final size:31
Alignment explanation
Indices: 261065--261126 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
261055 CCTCGACAAC
*
261065 TGTCCATAGGTCCCG-AAGAACCTAGGTAAAT
1 TGTCCATAGGTCCCGAAAG-ACATAGGTAAAT
* *
261096 TGTCCATATGTCTCGAAAGACATAGGTAAAT
1 TGTCCATAGGTCCCGAAAGACATAGGTAAAT
261127 CCTCAACTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 24 0.89
32 3 0.11
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (31 bp):
TGTCCATAGGTCCCGAAAGACATAGGTAAAT
Found at i:262095 original size:20 final size:20
Alignment explanation
Indices: 262070--262107 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
262060 TTCCCCTTGA
262070 AGTGCATCGATGCATTCTAT
1 AGTGCATCGATGCATTCTAT
*
262090 AGTGCATTGATGCATTCT
1 AGTGCATCGATGCATTCT
262108 TTAACATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAT
Found at i:262125 original size:24 final size:20
Alignment explanation
Indices: 262070--262127 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
262060 TTCCCCTTGA
*
262070 AGTGCATCGATGCATTCTAT
1 AGTGCATCGATGCATTCTAC
*
262090 AGTGCATTGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
262113 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
262128 CTACCCATGC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 16 0.52
22 1 0.03
23 2 0.06
24 12 0.39
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:271596 original size:23 final size:23
Alignment explanation
Indices: 271570--271614 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
271560 AAGCATTATT
*
271570 AAATTATAATTCT-ATTAAAAGTG
1 AAATTA-AATTATAATTAAAAGTG
271593 AAATTAAATTATAATTAAAAGT
1 AAATTAAATTATAATTAAAAGT
271615 TAATTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.38
Consensus pattern (23 bp):
AAATTAAATTATAATTAAAAGTG
Found at i:272083 original size:21 final size:20
Alignment explanation
Indices: 272049--272100 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
272039 CACGTTTTTA
* *
272049 TTTGTCTTTATGTCATATTT
1 TTTGTTTTTTTGTCATATTT
* *
272069 TCTTTTTTTTTTGTCATGTTT
1 T-TTGTTTTTTTGTCATATTT
272090 TTTGTTTTTTT
1 TTTGTTTTTTT
272101 AGCTGTTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.08, C:0.08, G:0.10, T:0.75
Consensus pattern (20 bp):
TTTGTTTTTTTGTCATATTT
Found at i:273467 original size:36 final size:36
Alignment explanation
Indices: 273426--273501 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
273416 ATTTTCGGGA
*
273426 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
273462 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
273498 TTTT
1 TTTT
273502 TTAGCTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:274156 original size:31 final size:31
Alignment explanation
Indices: 274120--274178 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
274110 ATAAAAGTGA
274120 AATTAAATAAAAACAAACGTGACTATATCTT
1 AATTAAATAAAAACAAACGTGACTATATCTT
* *
274151 AATTAAATAAAAATAAATGTGACTATAT
1 AATTAAATAAAAACAAACGTGACTATAT
274179 GTATATATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.54, C:0.08, G:0.07, T:0.31
Consensus pattern (31 bp):
AATTAAATAAAAACAAACGTGACTATATCTT
Found at i:274660 original size:22 final size:21
Alignment explanation
Indices: 274630--274672 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
274620 ATAACTTATT
*
274630 TATTATTATTTTATATATAAAA
1 TATTATTATTTTA-AAATAAAA
*
274652 TATTGTTATTTTAAAATAAAA
1 TATTATTATTTTAAAATAAAA
274673 CATTTCTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
TATTATTATTTTAAAATAAAA
Found at i:280769 original size:14 final size:14
Alignment explanation
Indices: 280752--280798 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
280742 GTCTTAGATC
280752 TTAAACCTTAAATT
1 TTAAACCTTAAATT
280766 TT-AACCTTTAAATT
1 TTAAACC-TTAAATT
*
280780 TTAAA-CTCTAAATC
1 TTAAACCT-TAAATT
280794 TTAAA
1 TTAAA
280799 TCTAAACCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
13 5 0.17
14 22 0.76
15 2 0.07
ACGTcount: A:0.43, C:0.15, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAACCTTAAATT
Found at i:282963 original size:30 final size:29
Alignment explanation
Indices: 282929--282986 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
282919 TCGATATATC
*
282929 ATCGGTGAACAGTATATTTTTTGATCTAAT
1 ATCGGT-AACAGTATATTTTTCGATCTAAT
* * *
282959 ATCGGTCAGATTATATTTTTCGATCTAA
1 ATCGGTAACAGTATATTTTTCGATCTAA
282987 CACCCTTAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.43
Consensus pattern (29 bp):
ATCGGTAACAGTATATTTTTCGATCTAAT
Found at i:283085 original size:51 final size:51
Alignment explanation
Indices: 283008--283129 Score: 142
Period size: 51 Copynumber: 2.4 Consensus size: 51
282998 GTAAAGTGCA
* * * *
283008 CCCCTTGCACCGCGCTATACGATGATTTGGCGCT-ACGTGGGGTATAGCGC-G
1 CCCCCTGCACCGCGCTATACGATGATTTGAC-ATAACGT-GAGTATAGCGCAG
*
283059 CCCCCTGCACCGCGCTATACGGTGATTTGACATACACGTGAGTATAGCGCAG
1 CCCCCTGCACCGCGCTATACGATGATTTGACATA-ACGTGAGTATAGCGCAG
*
283111 -CCCCTGCAACGCGCTATAC
1 CCCCCTGCACCGCGCTATAC
283130 CTGGATATCT
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
50 1 0.02
51 56 0.90
52 5 0.08
ACGTcount: A:0.20, C:0.33, G:0.26, T:0.21
Consensus pattern (51 bp):
CCCCCTGCACCGCGCTATACGATGATTTGACATAACGTGAGTATAGCGCAG
Found at i:283297 original size:13 final size:14
Alignment explanation
Indices: 283269--283297 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
283259 ATATTTTATA
283269 ATATTTTTACTATT
1 ATATTTTTACTATT
283283 ATATTTTTACT-TT
1 ATATTTTTACTATT
283296 AT
1 AT
283298 TTAATATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.66
Consensus pattern (14 bp):
ATATTTTTACTATT
Found at i:288454 original size:51 final size:51
Alignment explanation
Indices: 288378--288502 Score: 223
Period size: 51 Copynumber: 2.5 Consensus size: 51
288368 TTATACAAAA
* *
288378 CGCGGTACCTGCCCCACGCTATATAAAATTATGTGAGGAGTAAAGGTATGT
1 CGCGGTACCTGCCCCGCGCTATATAAAATTATGTCAGGAGTAAAGGTATGT
288429 CGCGGTACCTGCCCCGCGCTATATAAAATTATGTCAGGAGTAAAGGTATGT
1 CGCGGTACCTGCCCCGCGCTATATAAAATTATGTCAGGAGTAAAGGTATGT
*
288480 CGCGGTACCTGTCCCGCGCTATA
1 CGCGGTACCTGCCCCGCGCTATA
288503 CTCCTACGTG
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 71 1.00
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.25
Consensus pattern (51 bp):
CGCGGTACCTGCCCCGCGCTATATAAAATTATGTCAGGAGTAAAGGTATGT
Found at i:291286 original size:15 final size:15
Alignment explanation
Indices: 291266--291295 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
291256 ATCAGGCGGA
291266 GAGCCGAATGAATGG
1 GAGCCGAATGAATGG
291281 GAGCCGAATGAATGG
1 GAGCCGAATGAATGG
291296 AAACCGAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.40, T:0.13
Consensus pattern (15 bp):
GAGCCGAATGAATGG
Found at i:291302 original size:15 final size:15
Alignment explanation
Indices: 291269--291303 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
291259 AGGCGGAGAG
* *
291269 CCGAATGAATGGGAG
1 CCGAATGAATGGAAA
291284 CCGAATGAATGGAAA
1 CCGAATGAATGGAAA
291299 CCGAA
1 CCGAA
291304 AGGCAAGGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.40, C:0.17, G:0.31, T:0.11
Consensus pattern (15 bp):
CCGAATGAATGGAAA
Found at i:291702 original size:20 final size:20
Alignment explanation
Indices: 291677--291726 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
291667 GATCAACAAA
291677 TTCGCAACGCAAACTCCAAT
1 TTCGCAACGCAAACTCCAAT
* **
291697 TTCGCAACTCAATTTCCAAT
1 TTCGCAACGCAAACTCCAAT
291717 TTCGCAACGC
1 TTCGCAACGC
291727 GAATATGTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.30, C:0.34, G:0.10, T:0.26
Consensus pattern (20 bp):
TTCGCAACGCAAACTCCAAT
Found at i:291768 original size:21 final size:21
Alignment explanation
Indices: 291735--291784 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
291725 GCGAATATGT
*
291735 AAATT-GCATTGCGATTTTTC
1 AAATTCGCATTGCGATTTTCC
*
291755 AAATTCGCGTTGCGATTTTCC
1 AAATTCGCATTGCGATTTTCC
*
291776 AATTTCGCA
1 AAATTCGCA
291785 ACAGGAATCT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 5 0.20
21 20 0.80
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (21 bp):
AAATTCGCATTGCGATTTTCC
Found at i:291843 original size:20 final size:20
Alignment explanation
Indices: 291820--292004 Score: 125
Period size: 20 Copynumber: 9.0 Consensus size: 20
291810 AATTTATAAA
*
291820 TCGCAACACAGAAGTCAAAT
1 TCGCAACGCAGAAGTCAAAT
*
291840 TCGCAACACA-AAGTCAAAT
1 TCGCAACGCAGAAGTCAAAT
*
291859 TCGCAACGC-GATAGTCTAAT
1 TCGCAACGCAGA-AGTCAAAT
*
291879 TCGTAACGC-GAATTTGT-AAA-
1 TCGCAACGCAGAA---GTCAAAT
* *
291899 TCGCAACACATAAGTCAAAT
1 TCGCAACGCAGAAGTCAAAT
291919 TCGCAACGCA-ATAGTCAAAT
1 TCGCAACGCAGA-AGTCAAAT
*
291939 TCGCAATGC-GATAGTCAAAT
1 TCGCAACGCAGA-AGTCAAAT
*
291959 TCGCATTCGCAATGCGATAGTCAAAT
1 TCGCA-ACGC-A---GA-AGTCAAAT
291985 TCGCAACGC-GAAAGTCAAAT
1 TCGCAACGCAG-AAGTCAAAT
292005 GTTTTTACGC
Statistics
Matches: 136, Mismatches: 12, Indels: 34
0.75 0.07 0.19
Matches are distributed among these distances:
18 2 0.01
19 23 0.17
20 83 0.61
21 7 0.05
22 2 0.01
25 3 0.02
26 16 0.12
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (20 bp):
TCGCAACGCAGAAGTCAAAT
Found at i:291844 original size:40 final size:40
Alignment explanation
Indices: 291800--291929 Score: 147
Period size: 40 Copynumber: 3.3 Consensus size: 40
291790 AATCTGTAAA
291800 TCGCAACGCAAATTTATAAATCGCAACACAGAAGTCAAAT
1 TCGCAACGCAAATTTATAAATCGCAACACAGAAGTCAAAT
* * * * * *
291840 TCGCAACACAAAGTCA-AATTCGCAACGC-GATAGTCTAAT
1 TCGCAACGCAAATTTATAAATCGCAACACAGA-AGTCAAAT
* * * *
291879 TCGTAACGCGAATTTGTAAATCGCAACACATAAGTCAAAT
1 TCGCAACGCAAATTTATAAATCGCAACACAGAAGTCAAAT
291919 TCGCAACGCAA
1 TCGCAACGCAA
291930 TAGTCAAATT
Statistics
Matches: 69, Mismatches: 18, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
38 2 0.03
39 27 0.39
40 39 0.57
41 1 0.01
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.21
Consensus pattern (40 bp):
TCGCAACGCAAATTTATAAATCGCAACACAGAAGTCAAAT
Found at i:291893 original size:79 final size:80
Alignment explanation
Indices: 291804--291961 Score: 255
Period size: 79 Copynumber: 2.0 Consensus size: 80
291794 TGTAAATCGC
291804 AACGCAAATTTATAAATCGCAACACAGAAGTCAAATTCGCAACACAA-AGTCAAATTCGCAACGC
1 AACGCAAATTTATAAATCGCAACACAGAAGTCAAATTCGCAACACAATAGTCAAATTCGCAACGC
*
291868 GATAGTCTAATTCGT
66 GATAGTCAAATTCGT
* * * * *
291883 AACGCGAATTTGTAAATCGCAACACATAAGTCAAATTCGCAACGCAATAGTCAAATTCGCAATGC
1 AACGCAAATTTATAAATCGCAACACAGAAGTCAAATTCGCAACACAATAGTCAAATTCGCAACGC
291948 GATAGTCAAATTCG
66 GATAGTCAAATTCG
291962 CATTCGCAAT
Statistics
Matches: 72, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
79 43 0.60
80 29 0.40
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (80 bp):
AACGCAAATTTATAAATCGCAACACAGAAGTCAAATTCGCAACACAATAGTCAAATTCGCAACGC
GATAGTCAAATTCGT
Done.